#!/bin/bash
#PBS -l nodes=1:ppn=48,walltime=12:00:00,mem=10gb 
#PBS -N gsinghal_NA18489_YRI
#PBS -d /scratch/gsinghal/YRI_LC/
#PBS -q dque_smp 
bowtie2 -p 48  --sensitive -x  YRIref_index  -1 SRR003258_1.filt.fastq,SRR003259_1.filt.fastq,SRR003260_1.filt.fastq,SRR003261_1.filt.fastq,SRR003262_1.filt.fastq,SRR003263_1.filt.fastq,SRR003264_1.filt.fastq,SRR003265_1.filt.fastq,SRR003266_1.filt.fastq,SRR003267_1.filt.fastq,SRR018110_1.filt.fastq,SRR020466_1.filt.fastq,SRR020467_1.filt.fastq,SRR027536_1.filt.fastq -2 SRR003258_2.filt.fastq,SRR003259_2.filt.fastq,SRR003260_2.filt.fastq,SRR003261_2.filt.fastq,SRR003262_2.filt.fastq,SRR003263_2.filt.fastq,SRR003264_2.filt.fastq,SRR003265_2.filt.fastq,SRR003266_2.filt.fastq,SRR003267_2.filt.fastq,SRR018110_2.filt.fastq,SRR020466_2.filt.fastq,SRR020467_2.filt.fastq,SRR027536_2.filt.fastq -S NA18489_YRIref_index.sam &>  NA18489_YRIref_index_bowtie2.txt  
